Microbial drivers of ammonium accumulation in Holocene sediments of the Pearl River Delta

Delta ecosystems are critical zones connecting terrestrial and marine environments, with delta sediments preserving long-term records of land-sea interactions and environmental changes. The Pearl River Delta (PRD) is characterized by elevated ammonium levels in groundwater, posing risks to water quality and environmental health. This study investigates the microbial processes driving ammonium generation and accumulation across distinct depositional zones (terrestrial-dominated, transitional, and marine-dominated) in Holocene sediments of the PRD. Microbial communities exhibit stratification along environmental gradients. Bacterial communities (dominated by Pseudomonadota) reflect influences from both terrestrial and marine environments, while archaeal communities (led by Bathyarchaeia) resemble those in marine anaerobic ecosystems. Fermentation is the primary process driving ammonium production across all zones, with negligible ammonium consumption via nitrification and anammox. Secondary processes include nitrate reduction in terrestrial-dominated zones and dissimilatory nitrate reduction to ammonium (DNRA) in transitional and marine-dominated zones. Sulfate reduction predominating over nitrate reduction in marine-dominated zones. Brevirhabdus, a key bacterial contributor to fermentation and DNRA, links early marine deposition to ammonium dynamics in deltaic sediments. Environmental factors such as electrical conductivity (EC), carbon isotope composition (δ13C), and sediment depth strongly influence microbial community structure and function, emphasizing the critical role of geochemical processes in shaping microbial adaptation. Purifying selection dominates metabolic gene evolution, with functional genes related to sulfate and nitrate reduction highly conserved in marine-dominated zones, while fermentation genes exhibit depth-dependent. These findings reveal the interplay among depositional history, microbial adaptation, and biogeochemical processes, linking ammonium dynamics to climate-driven environmental changes, thus providing a framework to address groundwater quality risks in deltaic systems.